validateSamFile: A function to validate SAM or BAM files

In chimera: A package for secondary analysis of fusion products

Description

A function to validate SAM or BAM files using picard-tools

Usage

validateSamFile(input, output, mode=c("VERBOSE", "SUMMARY"), max.output="100")

Arguments

input	SAM/BAM file to be validated
output	file name in which to save the validation information
mode	Mode of output. Default value: VERBOSE
max.output	max number of reported error lines

Value

Validation information referring to a SAM/BM file.

Author(s)

Raffaele A Calogero

See Also

picardInstallation

Examples

#validateSamFile(input=paste(find.package(package="chimera"),"/examples/mcf7_trs_accepted_hits.bam",sep=""), output="validation_results.txt", mode="SUMMARY", max.output="100")

chimera documentation built on Nov. 8, 2020, 5:16 p.m.